{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1903ZZEJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1903ZZEJ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1903ZZEJ](/measurement-sets/IGVFDS1903ZZEJ/) has sequence file(s) [IGVFFI5855JQEM](/sequence-files/IGVFFI5855JQEM/), [IGVFFI0554NFJM](/sequence-files/IGVFFI0554NFJM/), [IGVFFI0456XDRV](/sequence-files/IGVFFI0456XDRV/), [IGVFFI2599PWZT](/sequence-files/IGVFFI2599PWZT/), [IGVFFI7500IIHI](/sequence-files/IGVFFI7500IIHI/), [IGVFFI7102RVTN](/sequence-files/IGVFFI7102RVTN/), [IGVFFI0581UNCQ](/sequence-files/IGVFFI0581UNCQ/), [IGVFFI7786PDBQ](/sequence-files/IGVFFI7786PDBQ/), [IGVFFI2119GFAZ](/sequence-files/IGVFFI2119GFAZ/), [IGVFFI7863MFAT](/sequence-files/IGVFFI7863MFAT/), [IGVFFI4223QPVZ](/sequence-files/IGVFFI4223QPVZ/), [IGVFFI0220IUQX](/sequence-files/IGVFFI0220IUQX/), [IGVFFI3973DVGN](/sequence-files/IGVFFI3973DVGN/), [IGVFFI1527ORNG](/sequence-files/IGVFFI1527ORNG/), [IGVFFI9549CUND](/sequence-files/IGVFFI9549CUND/), [IGVFFI8610JHJL](/sequence-files/IGVFFI8610JHJL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS1903ZZEJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1903ZZEJ](/measurement-sets/IGVFDS1903ZZEJ/) has sequence file(s): [IGVFFI5855JQEM](/sequence-files/IGVFFI5855JQEM/), [IGVFFI0554NFJM](/sequence-files/IGVFFI0554NFJM/), [IGVFFI0456XDRV](/sequence-files/IGVFFI0456XDRV/), [IGVFFI2599PWZT](/sequence-files/IGVFFI2599PWZT/), [IGVFFI7500IIHI](/sequence-files/IGVFFI7500IIHI/), [IGVFFI7102RVTN](/sequence-files/IGVFFI7102RVTN/), [IGVFFI0581UNCQ](/sequence-files/IGVFFI0581UNCQ/), [IGVFFI7786PDBQ](/sequence-files/IGVFFI7786PDBQ/), [IGVFFI2119GFAZ](/sequence-files/IGVFFI2119GFAZ/), [IGVFFI7863MFAT](/sequence-files/IGVFFI7863MFAT/), [IGVFFI4223QPVZ](/sequence-files/IGVFFI4223QPVZ/), [IGVFFI0220IUQX](/sequence-files/IGVFFI0220IUQX/), [IGVFFI3973DVGN](/sequence-files/IGVFFI3973DVGN/), [IGVFFI1527ORNG](/sequence-files/IGVFFI1527ORNG/), [IGVFFI9549CUND](/sequence-files/IGVFFI9549CUND/), [IGVFFI8610JHJL](/sequence-files/IGVFFI8610JHJL/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS1903ZZEJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1903ZZEJ](/measurement-sets/IGVFDS1903ZZEJ/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS1903ZZEJ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS8210FQOO/",
"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:39:23.946646+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5855JQEM/",
"accession": "IGVFFI5855JQEM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:21:44.099098+00:00",
"file_format": "fastq",
"file_size": 20142542,
"href": "/sequence-files/IGVFFI5855JQEM/@@download/IGVFFI5855JQEM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/3f4440af-35b7-483f-abf6-1b833a75eafc/IGVFFI5855JQEM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep2_S831_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0554NFJM/",
"accession": "IGVFFI0554NFJM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:24:57.767981+00:00",
"file_format": "fastq",
"file_size": 34831702,
"href": "/sequence-files/IGVFFI0554NFJM/@@download/IGVFFI0554NFJM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/57bda8cc-1b86-4805-8e87-29b4c1c4f081/IGVFFI0554NFJM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep3_S843_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0456XDRV/",
"accession": "IGVFFI0456XDRV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:27:23.823509+00:00",
"file_format": "fastq",
"file_size": 42318538,
"href": "/sequence-files/IGVFFI0456XDRV/@@download/IGVFFI0456XDRV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/67d0197f-aedd-47aa-87bf-1fbd3bbc9038/IGVFFI0456XDRV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep4_S855_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2599PWZT/",
"accession": "IGVFFI2599PWZT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:18:49.042517+00:00",
"file_format": "fastq",
"file_size": 34724972,
"href": "/sequence-files/IGVFFI2599PWZT/@@download/IGVFFI2599PWZT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/e8c86dc2-1615-40bc-82db-c8ca922115e1/IGVFFI2599PWZT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep1_S819_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7500IIHI/",
"accession": "IGVFFI7500IIHI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:17:55.167103+00:00",
"file_format": "fastq",
"file_size": 29676216,
"href": "/sequence-files/IGVFFI7500IIHI/@@download/IGVFFI7500IIHI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8f815072-ff90-4036-86b5-2b948938234e/IGVFFI7500IIHI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep3_S843_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7102RVTN/",
"accession": "IGVFFI7102RVTN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:19:38.143637+00:00",
"file_format": "fastq",
"file_size": 36444239,
"href": "/sequence-files/IGVFFI7102RVTN/@@download/IGVFFI7102RVTN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/99b8f7c2-7f7f-4e67-a312-8b8e1417adb0/IGVFFI7102RVTN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep4_S855_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0581UNCQ/",
"accession": "IGVFFI0581UNCQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:13:47.354450+00:00",
"file_format": "fastq",
"file_size": 30944672,
"href": "/sequence-files/IGVFFI0581UNCQ/@@download/IGVFFI0581UNCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/aafa0345-b878-450e-bfad-688edf3b6196/IGVFFI0581UNCQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep1_S819_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7786PDBQ/",
"accession": "IGVFFI7786PDBQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:15:49.160179+00:00",
"file_format": "fastq",
"file_size": 17909034,
"href": "/sequence-files/IGVFFI7786PDBQ/@@download/IGVFFI7786PDBQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/99176739-eee4-4754-a237-966ed5b1ec8f/IGVFFI7786PDBQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep2_S831_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2119GFAZ/",
"accession": "IGVFFI2119GFAZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:04:20.470066+00:00",
"file_format": "fastq",
"file_size": 7039452,
"href": "/sequence-files/IGVFFI2119GFAZ/@@download/IGVFFI2119GFAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/6d4f8d81-3fae-4ad7-99da-307c6f65f483/IGVFFI2119GFAZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep2_S831_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7863MFAT/",
"accession": "IGVFFI7863MFAT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:01:15.023736+00:00",
"file_format": "fastq",
"file_size": 12153687,
"href": "/sequence-files/IGVFFI7863MFAT/@@download/IGVFFI7863MFAT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/0d8c3347-ea40-41a9-99b3-09ad8aee6cef/IGVFFI7863MFAT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep1_S819_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4223QPVZ/",
"accession": "IGVFFI4223QPVZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:09:57.441324+00:00",
"file_format": "fastq",
"file_size": 15513779,
"href": "/sequence-files/IGVFFI4223QPVZ/@@download/IGVFFI4223QPVZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/fea9114c-be89-4c1e-a0da-42c7638bbdc2/IGVFFI4223QPVZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep4_S855_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0220IUQX/",
"accession": "IGVFFI0220IUQX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:14:05.744475+00:00",
"file_format": "fastq",
"file_size": 13260237,
"href": "/sequence-files/IGVFFI0220IUQX/@@download/IGVFFI0220IUQX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/29b955f8-9629-483c-ab41-8fa88488be43/IGVFFI0220IUQX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep1_S819_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3973DVGN/",
"accession": "IGVFFI3973DVGN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:07:25.839509+00:00",
"file_format": "fastq",
"file_size": 12617192,
"href": "/sequence-files/IGVFFI3973DVGN/@@download/IGVFFI3973DVGN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/7ce34a50-1580-4c52-9664-59235b76a216/IGVFFI3973DVGN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep3_S843_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1527ORNG/",
"accession": "IGVFFI1527ORNG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:22:35.219281+00:00",
"file_format": "fastq",
"file_size": 15659559,
"href": "/sequence-files/IGVFFI1527ORNG/@@download/IGVFFI1527ORNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/3e7c7b9f-2616-4465-8936-807ac51255e8/IGVFFI1527ORNG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep4_S855_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9549CUND/",
"accession": "IGVFFI9549CUND",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:17:09.423921+00:00",
"file_format": "fastq",
"file_size": 7733102,
"href": "/sequence-files/IGVFFI9549CUND/@@download/IGVFFI9549CUND.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/85a32541-352c-4bba-b6ec-c54e56628b12/IGVFFI9549CUND.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep2_S831_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8610JHJL/",
"accession": "IGVFFI8610JHJL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:20:06.318235+00:00",
"file_format": "fastq",
"file_size": 11724439,
"href": "/sequence-files/IGVFFI8610JHJL/@@download/IGVFFI8610JHJL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/5a01a8b1-bf24-4084-b002-59b5b562a2e1/IGVFFI8610JHJL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep3_S843_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8267JJHO/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0150ACKK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0150ACKK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinA"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9097TEUZ/",
"accession": "IGVFDS9097TEUZ",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-11T00:18:49.042517+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "7c6cbd77-becd-46b7-bdce-f8880b533fce"
}